Research workbench

SF3B core in complex with a splicing modulator

Analyse SF3B core in complex with a splicing modulator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EN4
Type: protein
Length: 2,180 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Splicing factor 3B subunit 3; Splicing factor 3B subunit 5; Splicing factor 3B subunit 1…
UniProt: Q15393, Q9BWJ5, O75533, Q7RTV0
Ligands: BGZ, ZN
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Splicing factor 3B subunit 3	protein	1180	8% helix, 48% strand	Q15393
B	Splicing factor 3B subunit 5	protein	65	58% helix, 0% strand	Q9BWJ5
C	Splicing factor 3B subunit 1	protein	842	76% helix, 0% strand	O75533
D	Phd finger-like domain-containing protein 5A	protein	93	12% helix, 29% strand	Q7RTV0

Ligands and binding sites

BGZ · [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{S})-6-methyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] ethanoate · ligand · chains C, D
ZN · Zinc ion · metal · 3 copies · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1125	0.84	0.85	81	empty
2	305	0.81	0.91	47	empty
3	828	0.80	0.83	55	empty
4	1128	0.77	0.79	107	empty
5	103	0.74	0.96	23	empty

Interfaces

5 interfaces between chains.

A–B · 2362 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 2358 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1567 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1326 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 588 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6EN4 · SF3b core in complex with a splicing modulator · the same entry in another collection · chain D against D, TM-score 1.00
Q9BWJ5 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 5 (Q9BWJ5) · a predicted model of the same protein · chain B against A, TM-score 0.92
Q7RTV0 · AlphaFold monomer V2.0 prediction for phd finger-like domain- containing protein 5A… · a predicted model of the same protein · chain D against A, TM-score 0.89
Q15393 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 3 (Q15393) · a predicted model of the same protein · chain A against A, TM-score 0.83
O75533 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 1 (O75533) · a predicted model of the same protein · chain C against A, TM-score 0.81

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q15393
Every structure of UniProt Q9BWJ5
Every structure of UniProt O75533
Every structure of UniProt Q7RTV0
Elsewhere: RCSB PDB 6EN4 · PDBe 6EN4 · UniProt Q15393 · UniProt Q9BWJ5 · UniProt O75533 · UniProt Q7RTV0

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